Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Björn Grüning]

Sounds great Hans,

gfortran is only needed on OS-X for Linux we can ship precompiled
binaries. Moreover if you setup your production instance keep this list
in mind.

https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList

Cheers,
Bjoern

> Hi Marius,
> 
> I bow to your efforts in appreciation - it seems to install without
> flaws!!
> 
> I tried the new cairo-1-12-14 and then r-3-2-1 in a frest
> postgresqldb/galaxy instance … everything got installed and shows the
> green label ;-)
> 
> requirements on top of Mac OS Xcode/command line tools are: -
> gfortran (I used the OS X 10.11  gfortran 5.2 installer from here
> https://gcc.gnu.org/wiki/GFortranBinaries
> ) - libiconv-1.14 (from
> http://ftp.gnu.org/pub/gnu/libiconv/libiconv-1.14.tar.gz
> ) - (which
> I put into /usr/local where it seems to be found without editing my
> $PATH)
> 
> This is great! Many thanks again! Hans
> 
> 
> 
> 
> 
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Hi,

I now learned that R-3.2.2 binaries for Mac OS X are available 
(https://cran.r-project.org/bin/macosx/) - could that be a potential help for 
R-related problems in galaxy on Mac OS X?

Cheers,
Hans
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Marius van den Beek]

Hello Hans,

I'm not sure if it would help to use the pre-compiled binaries,
as you would still need some of the underlying libraries for building
R packages. We're not far from having this fixed ... there is a newer
revision of R on the main toolshed,
that nevertheless will (probably) fail because of a missing include of what
seems to be fontconfig.
I had it working yesterday already, I'm trying to see what went wrong in
the meantime ...

Marius

On 4 December 2015 at 09:20, Hans Rudolph  wrote:

> Hi,
>
> I now learned that R-3.2.2 binaries for Mac OS X are available (
> https://cran.r-project.org/bin/macosx/) - could that be a potential help
> for R-related problems in galaxy on Mac OS X?
>
> Cheers,
> Hans
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Marius van den Beek]

Hello Hans (and other OS X users),

I hope that the last remaining problem should be fixed now.
There is a new revision of package_r_3_2_1 and package_cairo_1_12_14 on the
toolshed.
Make sure you get package_cairo_1_12_14 first when you upgrade.
The underlying problem was that cairo was missing the fontconfig dependency,
which would still compile correctly, but fail when R is built with
`--with-cairo`.

Cheers,
Marius

On 4 December 2015 at 09:47, Marius van den Beek 
wrote:

> Hello Hans,
>
> I'm not sure if it would help to use the pre-compiled binaries,
> as you would still need some of the underlying libraries for building
> R packages. We're not far from having this fixed ... there is a newer
> revision of R on the main toolshed,
> that nevertheless will (probably) fail because of a missing include of
> what seems to be fontconfig.
> I had it working yesterday already, I'm trying to see what went wrong in
> the meantime ...
>
> Marius
>
> On 4 December 2015 at 09:20, Hans Rudolph  wrote:
>
>> Hi,
>>
>> I now learned that R-3.2.2 binaries for Mac OS X are available (
>> https://cran.r-project.org/bin/macosx/) - could that be a potential help
>> for R-related problems in galaxy on Mac OS X?
>>
>> Cheers,
>> Hans
>
>
>
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Martin Čech]

Awesome Marius, thank you very much for looking into this! M.

On Fri, Dec 4, 2015 at 12:30 PM Marius van den Beek 
wrote:

> Hello Hans (and other OS X users),
>
> I hope that the last remaining problem should be fixed now.
> There is a new revision of package_r_3_2_1 and package_cairo_1_12_14 on
> the toolshed.
> Make sure you get package_cairo_1_12_14 first when you upgrade.
> The underlying problem was that cairo was missing the fontconfig
> dependency,
> which would still compile correctly, but fail when R is built with
> `--with-cairo`.
>
> Cheers,
> Marius
>
> On 4 December 2015 at 09:47, Marius van den Beek 
> wrote:
>
>> Hello Hans,
>>
>> I'm not sure if it would help to use the pre-compiled binaries,
>> as you would still need some of the underlying libraries for building
>> R packages. We're not far from having this fixed ... there is a newer
>> revision of R on the main toolshed,
>> that nevertheless will (probably) fail because of a missing include of
>> what seems to be fontconfig.
>> I had it working yesterday already, I'm trying to see what went wrong in
>> the meantime ...
>>
>> Marius
>>
>> On 4 December 2015 at 09:20, Hans Rudolph  wrote:
>>
>>> Hi,
>>>
>>> I now learned that R-3.2.2 binaries for Mac OS X are available (
>>> https://cran.r-project.org/bin/macosx/) - could that be a potential
>>> help for R-related problems in galaxy on Mac OS X?
>>>
>>> Cheers,
>>> Hans
>>
>>
>>
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Hi,

not sure whether that helps, but I tried to compile r-3-2-1 outside galaxy on 
the same machine:

1.straight ./configure yields error: "cannot compile a simple Fortran program."
To remedie this, I installed gfortran (=gf) 5.2 for OS X (10.11) from 
https://gcc.gnu.org/wiki/GFortranBinaries 


and with gf installed, ./configure now completes, but make fails with "dyld: 
Symbol not found: _libiconv_open"

2. I then installed libiconv-1.4 as suggested in this tip for R-on-OS X: 
http://blog.qiubio.com:8080/archives/3897 

and put /usr/local/lib into $PATH
now make finishes …


I made mistakes running ./configure and make/install
first omitting the epxort LD_LIBRARY_PATH= command … and I don’t have proper 
records ;-)

Not sure how to clean this up - but I wanted to let you know my findings with 
respect to compiling r-3-2-1

Cheers,

Hans



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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Marius van den Beek]

I opened a new PR here https://github.com/galaxyproject/tools-iuc/pull/459.
This adds the last remaining LD_INCLUDE_PATH's and as a side effect should
also help people with cairo problems.
Note that, at the core, Hans' problem stem from an outdated version of
fontconfig on the main toolshed, that is not setting FONTCONFIG_LIB_PATH
and FONTCONFIG_INCLUDE_PATH,
so updating fontconfig would suffice to get R compiling.
But let's accept the PR and move away from relying on arbitrarily named ENV
vars that are subject to change ...

On 3 December 2015 at 09:44, Marius van den Beek 
wrote:

> I could reproduce this, and in fact removing all the export statements
> would solve the problem.
> Those shouldn't be necessary in the first place since we consequently
> modify LD_INCLUDE_PATH and LD_LIBRARY_PATH.
> I have no proof yet, but I think the underlying problem is that OS Xs GCC
> compiler doesn't tolerate empty include or library PATHs. Probably one of
> the variables in the export statement is missing because it was renamed or
> removed. Yet, it would be much less maintenance work to rely on modified
> LD_INCLUDE_PATH and LD_LIBRARY_PATH and use the autoconf action.
> What do you think about this, Bjoern?
>
> Marius
>
> On 3 December 2015 at 09:21, Marius van den Beek 
> wrote:
>
>> Hi Hans,
>>
>> I've seen this error ("
>> configure: error: C compiler cannot create executables”) quite a few
>> times on OS X, and contrary to the message, is usually not related to the
>> installed compiler (all your other packages compiled just fine). I'll check
>> this on my macs, to see if we didn't introduce a regression. My feeling is
>> that one of the include PATHS hasn't been set correctly. Could you post the
>> full INSTALLATION.log ?
>>
>> Marius
>>
>> On 3 December 2015 at 00:49, Hans Rudolph  wrote:
>>
>>> Hi Björn,
>>>
>>> thanks very much for your efforts. Unfortunately, installation of the
>>> new deseq2-1-8-2 (uic, 2015-12-02) still fails for me -
>>>
>>> apparently due to the included package_r_3_2_1 which fails with "
>>> configure: error: C compiler cannot create executables”
>>> and the R error status stops deseq2 installation with error "
>>> /bin/sh: line 7: Rscript: command not found”.
>>>
>>> But all the other dependencies in the deseq2-1-8-2 package:
>>>
>>> atlas-3-10
>>> cairo-1-12-14
>>> fontconfig-2-11-1
>>> freetype-2-5-2
>>> libpng-1-6-7
>>> libxml2-2-9-1
>>> ncurses-6-0
>>> pixman-0.32-4
>>> pixman-0-32-6
>>> readline-6-3
>>>
>>> show the green label “installed” as installation status.
>>>
>>> Best regards,
>>> Hans
>>>
>>>
>>>
>>>
>>>
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>>>   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Marius van den Beek]

I could reproduce this, and in fact removing all the export statements
would solve the problem.
Those shouldn't be necessary in the first place since we consequently
modify LD_INCLUDE_PATH and LD_LIBRARY_PATH.
I have no proof yet, but I think the underlying problem is that OS Xs GCC
compiler doesn't tolerate empty include or library PATHs. Probably one of
the variables in the export statement is missing because it was renamed or
removed. Yet, it would be much less maintenance work to rely on modified
LD_INCLUDE_PATH and LD_LIBRARY_PATH and use the autoconf action.
What do you think about this, Bjoern?

Marius

On 3 December 2015 at 09:21, Marius van den Beek 
wrote:

> Hi Hans,
>
> I've seen this error ("
> configure: error: C compiler cannot create executables”) quite a few
> times on OS X, and contrary to the message, is usually not related to the
> installed compiler (all your other packages compiled just fine). I'll check
> this on my macs, to see if we didn't introduce a regression. My feeling is
> that one of the include PATHS hasn't been set correctly. Could you post the
> full INSTALLATION.log ?
>
> Marius
>
> On 3 December 2015 at 00:49, Hans Rudolph  wrote:
>
>> Hi Björn,
>>
>> thanks very much for your efforts. Unfortunately, installation of the new
>> deseq2-1-8-2 (uic, 2015-12-02) still fails for me -
>>
>> apparently due to the included package_r_3_2_1 which fails with "
>> configure: error: C compiler cannot create executables”
>> and the R error status stops deseq2 installation with error "
>> /bin/sh: line 7: Rscript: command not found”.
>>
>> But all the other dependencies in the deseq2-1-8-2 package:
>>
>> atlas-3-10
>> cairo-1-12-14
>> fontconfig-2-11-1
>> freetype-2-5-2
>> libpng-1-6-7
>> libxml2-2-9-1
>> ncurses-6-0
>> pixman-0.32-4
>> pixman-0-32-6
>> readline-6-3
>>
>> show the green label “installed” as installation status.
>>
>> Best regards,
>> Hans
>>
>>
>>
>>
>>
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
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>>
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>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Martin Čech]

Hans:

I have had trouble with el capitan and gcc lately, updating the xcode
commandlinetools sometimes helps.

$ xcode-select --install

M.

On Wed, Dec 2, 2015 at 7:30 PM Hans Rudolph  wrote:

> Hi,
>
> I use Mac OS X 10.11.1 (El Capitan) - I append terminal output during the
> r-package installation and R INSTALLATION.LOG
> Cheers,
> Hans
>
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Hi,

I use Mac OS X 10.11.1 (El Capitan) - I append terminal output during the 
r-package installation and R INSTALLATION.LOG
Cheers,
Hans

tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2015-12-02 
23:04:16,463 Successfully downloaded from url: 
http://cran.rstudio.com/src/base/R-3/R-3.2.1.tar.gz
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,017 checking host system 
type... x86_64-apple-darwin15.0.0
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,031 loading build-specific 
script './config.site'
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,049 checking whether 
builddir is srcdir... yes
checking build system type... x86_64-apple-darwin15.0.0
checking host system type... x86_64-apple-darwin15.0.0
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,221 checking for working 
autoconf... found
checking for working aclocal... found
checking for working autoconf... found
checking for working automake... found
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,519 checking for working 
autoheader... found
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,526 checking for mawk... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,526 checking for awk... awk
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,526 checking for bison... 
bison -y
checking for working autoheader... found
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether ln -s works... yes
checking for bison... bison -y
checking for ar... ar
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,557 checking for a 
BSD-compatible install... /usr/bin/install -c
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,560 checking for which... 
/usr/bin/which
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,564 checking for gtar... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,565 checking for tar... 
/usr/bin/tar
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,568 checking for pdftex... 
no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,575 checking for 
makeindex... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,576 checking for 
texi2dvi... /usr/bin/texi2dvi
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,580 checking for latex 
inconsolata package... checking for unzip... /usr/bin/unzip
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,583 checking for gzip... 
/usr/bin/gzip
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,585 checking for 
firefox... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,588 checking for galeon... 
no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,591 checking for 
xdg-open... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,593 checking for 
gnome-moz-remote... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,595 using default browser 
... /usr/bin/open
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,598 checking for 
acroread4... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,600 checking for evince... 
no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,603 checking for gv... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,606 checking for ggv... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,608 checking for kpdf... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,612 checking for 
notangle... false
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,616 checking for 
pkg-config... /opt/local/bin/pkg-config
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /usr/bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... no
checking for gnutar... no
checking for tar... /usr/bin/tar
checking for tex... no
checking for pdftex... no
checking for pdflatex... no
checking for makeindex... no
checking for texi2any... no
checking for texi2dvi... /usr/bin/texi2dvi
checking for kpsewhich... no
checking for latex inconsolata package... checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /usr/bin/gzip
checking for bzip2... /opt/local/bin/bzip2
checking for firefox... no
checking for mozilla... no
checking for galeon... no
checking for opera... no
checking for xdg-open... no
checking for kfmclient... no
checking for gnome-moz-remote... no
checking for open... /usr/bin/open
using default browser ... /usr/bin/open
checking for acroread... no
checking for acroread4... no
checking for xdg-open... no
checking for evince... no
checking for xpdf... no
checking for gv... no
checking for gnome-gv... no
checking for ggv... no
checking for okular... no
checking for kpdf... no
checking for open... /usr/bin/open
checking for notangle... false
checking for realpath... false
checking for pkg-config... /opt/local/bin/pkg-config
checking for gcc... gcc

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Hi,
I hope I am up-to-date:
$ xcode-select —install yields:
xcode-select: error: command line tools are already installed, use "Software 
Update" to install updates

and software-update doesn’t show anything

Cheers,
Hans___
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Björn Grüning]

Hi Hans,

as non-Apple user I now a little bit lost here.

Can you please read this one:
http://stackoverflow.com/questions/10357804/configure-error-c-compiler-cannot-create-executables

It seems to be a fruit problem :)
The error message is not so meaningful than I had hoped.

Cheers,
Bjoern

Am 03.12.2015 um 01:30 schrieb Hans Rudolph:
> Hi,
> 
> I use Mac OS X 10.11.1 (El Capitan) - I append terminal output during the 
> r-package installation and R INSTALLATION.LOG
> Cheers,
> Hans
> 
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Björn Grüning]

Hi,

which operating system are you using? We ship precompiled binaries for
x64-linux systems. So I wonder why your Galaxy is trying to compile R.

Can you provide us with the INSTALLATION.log from the R package?

Thanks,
Bjoern

Am 03.12.2015 um 00:49 schrieb Hans Rudolph:
> Hi Björn,
> 
> thanks very much for your efforts. Unfortunately, installation of the new 
> deseq2-1-8-2 (uic, 2015-12-02) still fails for me -
> 
> apparently due to the included package_r_3_2_1 which fails with "configure: 
> error: C compiler cannot create executables”
> and the R error status stops deseq2 installation with error "/bin/sh: line 7: 
> Rscript: command not found”.
> 
> But all the other dependencies in the deseq2-1-8-2 package:
> 
> atlas-3-10
> cairo-1-12-14
> fontconfig-2-11-1
> freetype-2-5-2
> libpng-1-6-7
> libxml2-2-9-1
> ncurses-6-0
> pixman-0.32-4
> pixman-0-32-6
> readline-6-3
> 
> show the green label “installed” as installation status.
> 
> Best regards,
> Hans
> 
> 
> 
> 
> 
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Hi Björn,

thanks very much for your efforts. Unfortunately, installation of the new 
deseq2-1-8-2 (uic, 2015-12-02) still fails for me -

apparently due to the included package_r_3_2_1 which fails with "configure: 
error: C compiler cannot create executables”
and the R error status stops deseq2 installation with error "/bin/sh: line 7: 
Rscript: command not found”.

But all the other dependencies in the deseq2-1-8-2 package:

atlas-3-10
cairo-1-12-14
fontconfig-2-11-1
freetype-2-5-2
libpng-1-6-7
libxml2-2-9-1
ncurses-6-0
pixman-0.32-4
pixman-0-32-6
readline-6-3

show the green label “installed” as installation status.

Best regards,
Hans




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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Björn Grüning]

Hi,

we just did not updated the packages. Sorry. I have now pushed
everything to the TS's.

Hopefully it is working now for you.
Cheers,
Bjoern


> Thanks to Marius and Martin for fixing pixman-0.32.4!
> 
> This new pixman-0.32.4 version (owned by devteam) is also used by the
> new devteam cairo-1-12-14 package … both installed properly into
> galaxy on OS X.
> 
> I am curious/unclear on how to proceed with other packages, e.g.
> deseq2-1-8-2 (uic), which still seem to use the "old" cairo-1-12-14
> (uic) and pixman-0-32-4 (uic) versions … which won’t work on OS X.
> 
> What am I missing?
> 
> Best regards, Hans
> 
> 
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Martin Čech]

Hans Rudolph,

thanks to Marius van den Beek this issue should be fixed with this PR:
https://github.com/galaxyproject/tools-devteam/pull/299

These changes were already propagated to the Main Tool Shed.

Note for tool developers: for future endeavours please use packages from
the IUC repository (
https://github.com/galaxyproject/tools-iuc/tree/master/packages)

Thank you for the report (and for using Galaxy :)).

Martin


On Tue, Dec 1, 2015 at 6:25 AM Hans Rudolph  wrote:

> Hello Galaxy-devs,
>
> I am setting up galaxy on current os x 10.11 and encounter this trouble
> using galaxy to install pixman-0.32.4:
> the package gets downloaded successfully from
> http://cairographics.org/releases/pixman-0.32.4.tar.gz
> … while following the installation process in terminal I see this output
> during the process …presumably indicating an gcc problem
> ...
> install_environment.STDOUT DEBUG 2015-12-01 10:44:18,096 checking build
> system type... x86_64-apple-darwin15.0.0
> install_environment.STDOUT DEBUG 2015-12-01 10:44:18,099 checking for
> gcc... gcc
> checking build system type... x86_64-apple-darwin15.0.0
> checking host system type... x86_64-apple-darwin15.0.0
> checking for gcc... gcc
> checking whether the C compiler works... no
> configure: error: in
> `/Users/hans/galaxy/database/tmp/tmp-toolshed-mtdKC9F_F/pixman-0.32.4':
> configure: error: C compiler cannot create executables
> See `config.log' for more details
>
> Curiously, if I download the pixman package (same URL) outside of galaxy
> and run ./configure … gcc seems to work :
> ...
> checking build system type... x86_64-apple-darwin15.0.0
> checking host system type... x86_64-apple-darwin15.0.0
> checking for gcc... gcc
> checking whether the C compiler works… yes
> ...
> and ./configure finishes OK.
>
> to actually compile/make pixman properly, I have to use the ./configure
> —disable-mmx option to avoid another known error
> (*pixman-mmx.c:100:20: **error: **constraint 'K' expects an integer
> constant expression*
> : "y" (__A), "K" (__N))
>
> Perhaps someone is using galaxy on Mac OS X how this difference in gcc
> handling arises?
> Thanks very much,
>
> Hans Rudolph
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